If you heavily starch your quilt top before layering (as heavily as possible, as in several layers of spray starch allowing to dry in-between), this helps prevent the problem. Even now you can help the top by adding several layers of spray starch. Lay the quilt out on the floor on a large flat sheet to catch overspray, mist the top with spray starch, allow to dry (a fan speeds it up), mist again, let dry, etc. In other words, you don't have to iron. What the spray does is stabilize the fabric in the top so it is much less likely to get stretched while sewing. (Since you are not getting puckers on the back, I am wondering if the backing is unwashed fabric that still has the sizing in it; this too helps stabilize fabric and prevent it from stretching as you sew.)
The problem you are having is that the top fabric is stretching just a tiny bit with each stitch; by the time you get to where you need to cross the previous quilting line, a little bubble of fabric is between the needle and the line. This creates a pucker.
Since 60% or so of the time you are not getting the pucker, I think the spray starch misting several times may eliminate the problem for you.
If your machine allows you to ease up on the pressure, this might help too. If you ease up too much, though, you may start getting "tiny stitch syndrome" where the walking foot stops advancing the layers (a problem which is also created by drag).